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New module: BBDuk #1742

Merged
merged 13 commits into from Jan 8, 2023
Merged

New module: BBDuk #1742

merged 13 commits into from Jan 8, 2023

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jfy133
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@jfy133 jfy133 commented Aug 11, 2022

This is a standalone module from BBMap, which partly uses in BBDuk, however BBDuk 'standalone' produces different stdout (log) files, thus the module.

  • There is example tool output for tools in the https://github.com/ewels/MultiQC_TestData repository or attached to this PR: Add test data for BBduk test-data#239
  • Code is tested and works locally (including with --lint flag)
  • docs/README.md is updated with link to below
  • docs/modulename.md is created
  • Everything that can be represented with a plot instead of a table is a plot
  • Report sections have a description and help text (with self.add_section)
  • There aren't any huge tables with > 6 columns (explain reasoning if so)
  • Each table column has a different colour scale to its neighbour, which relates to the data (eg. if high numbers are bad, they're red)
  • Module does not do any significant computational work

@ewels
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ewels commented Jan 8, 2023

Ok, I've made quite a lot of changes here so please have a thorough review if you can.

  • Rewrote the log parsing to use regexes, and to parse the base numbers as well as read counts
  • Take the sample name from the first input file name, rather than the log file name
  • Removed most General Stats columns
  • Added the filtering types to the bar plot
  • Added base count as a second dataset to the bar plot
  • Removed the beeswarm plot

Let me know what you think!

@ewels ewels merged commit ee966ba into MultiQC:master Jan 8, 2023
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2 participants